Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 60 of 187
Found at i:17633465 original size:9 final size:9
Alignment explanation
Indices: 17633443--17633491 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
17633433 TAAAGTAAAT
*
17633443 AAAAGAAAC
1 AAAAGAAAG
*
17633452 TAAAGAAAG
1 AAAAGAAAG
17633461 AAAAGAAAG
1 AAAAGAAAG
17633470 AAAAG-AAG
1 AAAAGAAAG
*
17633478 TAAAAGAAAC
1 -AAAAGAAAG
17633488 AAAA
1 AAAA
17633492 AGAACAGCAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
8 3 0.09
9 29 0.85
10 2 0.06
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.04
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:17633491 original size:18 final size:19
Alignment explanation
Indices: 17633442--17633491 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
17633432 ATAAAGTAAA
*
17633442 TAAAAGAAACTAAAGAAAG
1 TAAAAGAAACAAAAGAAAG
*
17633461 -AAAAGAAAGAAAAG-AAG
1 TAAAAGAAACAAAAGAAAG
17633478 TAAAAGAAACAAAA
1 TAAAAGAAACAAAA
17633492 AGAACAGCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 3 0.11
18 24 0.89
ACGTcount: A:0.74, C:0.04, G:0.16, T:0.06
Consensus pattern (19 bp):
TAAAAGAAACAAAAGAAAG
Found at i:17634011 original size:3 final size:3
Alignment explanation
Indices: 17634003--17634057 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
17633993 TAATTAATAG
17634003 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
17634051 TAT TAT T
1 TAT TAT T
17634058 TTCGTAGCTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:17634480 original size:23 final size:23
Alignment explanation
Indices: 17634453--17634530 Score: 97
Period size: 23 Copynumber: 3.5 Consensus size: 23
17634443 GGCCTTGCCG
* *
17634453 ATCAGACACTTTATGTGTCGTAT
1 ATCAGGCACTTTATATGTCGTAT
17634476 ATCAGGCACTTTATATGTCGTAT
1 ATCAGGCACTTTATATGTCGTAT
* * *
17634499 TTCAGGCACCTCATATGTCGT-T
1 ATCAGGCACTTTATATGTCGTAT
17634521 -TCAGGCACTT
1 ATCAGGCACTT
17634531 ATGTGTCATA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
21 9 0.18
22 1 0.02
23 39 0.80
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (23 bp):
ATCAGGCACTTTATATGTCGTAT
Found at i:17640946 original size:34 final size:34
Alignment explanation
Indices: 17640897--17640962 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
17640887 CATCATTTAC
* *
17640897 TGCCAAGCAATAACTCCA-TTGACAATAATAGAAA
1 TGCCAAGAAAGAACTCCACTT-ACAATAATAGAAA
17640931 TGCCAAGAAAGAACTCCACTTACAATAATAGA
1 TGCCAAGAAAGAACTCCACTTACAATAATAGA
17640963 CACCCTACCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 27 0.93
35 2 0.07
ACGTcount: A:0.47, C:0.21, G:0.12, T:0.20
Consensus pattern (34 bp):
TGCCAAGAAAGAACTCCACTTACAATAATAGAAA
Found at i:17642664 original size:12 final size:12
Alignment explanation
Indices: 17642647--17642671 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17642637 ATTATTTCCA
17642647 TAAAAAAAAAAT
1 TAAAAAAAAAAT
17642659 TAAAAAAAAAAT
1 TAAAAAAAAAAT
17642671 T
1 T
17642672 TAAATCCTGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (12 bp):
TAAAAAAAAAAT
Found at i:17644442 original size:22 final size:22
Alignment explanation
Indices: 17644399--17644442 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
17644389 TTTTAAGTTA
*
17644399 CCCAAATAAGTGATCAACACAT
1 CCCAAATAAGTGATCAAAACAT
*
17644421 CCCAAA-ATGTGATCAATAACAT
1 CCCAAATAAGTGATCAA-AACAT
17644443 ACACTCTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.45, C:0.25, G:0.09, T:0.20
Consensus pattern (22 bp):
CCCAAATAAGTGATCAAAACAT
Found at i:17645706 original size:20 final size:20
Alignment explanation
Indices: 17645681--17645719 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
17645671 GTGTTGAATA
17645681 ATATTTTTAATAAA-TAATTT
1 ATATTTTTAA-AAATTAATTT
17645701 ATATTTTTAAAAATTAATT
1 ATATTTTTAAAAATTAATT
17645720 AATTATTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATATTTTTAAAAATTAATTT
Found at i:17646611 original size:14 final size:14
Alignment explanation
Indices: 17646592--17646618 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17646582 ATAATCTATC
17646592 GTTGTTGCCTTACT
1 GTTGTTGCCTTACT
17646606 GTTGTTGCCTTAC
1 GTTGTTGCCTTAC
17646619 AGTTCCATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.22, G:0.22, T:0.48
Consensus pattern (14 bp):
GTTGTTGCCTTACT
Found at i:17646668 original size:59 final size:59
Alignment explanation
Indices: 17646576--17646694 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
17646566 GTTCAAAACC
17646576 TTGTTTATAATCTATCGTTGTTGCCTTACTGTTGTTGCCTTACAGTTCCATTTGTTTAG
1 TTGTTTATAATCTATCGTTGTTGCCTTACTGTTGTTGCCTTACAGTTCCATTTGTTTAG
*
17646635 TTGTTTATAATCTGTCGTTGTTGCCTTACTGTTGTTGCCTTACAGTTCCATTTGTTTAG
1 TTGTTTATAATCTATCGTTGTTGCCTTACTGTTGTTGCCTTACAGTTCCATTTGTTTAG
17646694 T
1 T
17646695 CGTTCAAAAG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.14, C:0.17, G:0.18, T:0.51
Consensus pattern (59 bp):
TTGTTTATAATCTATCGTTGTTGCCTTACTGTTGTTGCCTTACAGTTCCATTTGTTTAG
Found at i:17646670 original size:14 final size:14
Alignment explanation
Indices: 17646651--17646677 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17646641 ATAATCTGTC
17646651 GTTGTTGCCTTACT
1 GTTGTTGCCTTACT
17646665 GTTGTTGCCTTAC
1 GTTGTTGCCTTAC
17646678 AGTTCCATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.22, G:0.22, T:0.48
Consensus pattern (14 bp):
GTTGTTGCCTTACT
Found at i:17646878 original size:12 final size:12
Alignment explanation
Indices: 17646861--17646890 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
17646851 TATTTGAAAT
*
17646861 TTTATATTCTGG
1 TTTATAATCTGG
17646873 TTTATAATCTGG
1 TTTATAATCTGG
17646885 TTTATA
1 TTTATA
17646891 CCTTGTTGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.07, G:0.13, T:0.57
Consensus pattern (12 bp):
TTTATAATCTGG
Found at i:17646885 original size:59 final size:59
Alignment explanation
Indices: 17646814--17646982 Score: 311
Period size: 59 Copynumber: 2.9 Consensus size: 59
17646804 TATCTTAAAT
* *
17646814 TTTATAATCTGGTTTATACCTTATTGCTTCTTTTTTATATTTGAAATTTTATATTCTGG
1 TTTATAATCTGGTTTATACCTTGTTGCTTCTTTTTTATATTTGAAATTTTATATTCTAG
*
17646873 TTTATAATCTGGTTTATACCTTGTTGCTTCTTTTTTATATCTGAAATTTTATATTCTAG
1 TTTATAATCTGGTTTATACCTTGTTGCTTCTTTTTTATATTTGAAATTTTATATTCTAG
17646932 TTTATAATCTGGTTTATACCTTGTTGCTTCTTTTTTATATTTGAAATTTTA
1 TTTATAATCTGGTTTATACCTTGTTGCTTCTTTTTTATATTTGAAATTTTA
17646983 AGCTCATTAT
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 106 1.00
ACGTcount: A:0.22, C:0.11, G:0.10, T:0.57
Consensus pattern (59 bp):
TTTATAATCTGGTTTATACCTTGTTGCTTCTTTTTTATATTTGAAATTTTATATTCTAG
Found at i:17650442 original size:18 final size:19
Alignment explanation
Indices: 17650419--17650467 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
17650409 GTTGTAAAGT
*
17650419 TTTATTTTTATTTATTTA-
1 TTTATTTTTATTTACTTAG
17650437 TTTATTTATT-TTTACTTAG
1 TTTATTT-TTATTTACTTAG
17650456 TTTAATTTTTAT
1 TTT-ATTTTTAT
17650468 GTAAATATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 7 0.27
20 5 0.19
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTATTTTTATTTACTTAG
Found at i:17650447 original size:22 final size:22
Alignment explanation
Indices: 17650418--17650467 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
17650408 AGTTGTAAAG
* *
17650418 TTTTATTTTTATTTA-TTTATT
1 TTTTATTTTTACTTAGTTTAAT
17650439 TATTTATTTTTACTTAGTTTAAT
1 T-TTTATTTTTACTTAGTTTAAT
17650462 TTTTAT
1 TTTTAT
17650468 GTAAATATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 18 0.72
23 6 0.24
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTATTTTTACTTAGTTTAAT
Found at i:17657339 original size:14 final size:15
Alignment explanation
Indices: 17657320--17657360 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
17657310 GTTGTAAAGT
17657320 TTTATTTTTATTTA-
1 TTTATTTTTATTTAG
*
17657334 TTTATTTTTACTTAG
1 TTTATTTTTATTTAG
17657349 TTTAATTTTTAT
1 TTT-ATTTTTAT
17657361 GTAAATATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 13 0.57
15 3 0.13
16 7 0.30
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (15 bp):
TTTATTTTTATTTAG
Found at i:17678145 original size:10 final size:11
Alignment explanation
Indices: 17678129--17678161 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
17678119 TTTTGAATAA
17678129 AATATTTTTTT
1 AATATTTTTTT
17678140 -ATATTTTTTT
1 AATATTTTTTT
17678150 AATAATTTTTTT
1 AAT-ATTTTTTT
17678162 TAAAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 2 0.10
12 8 0.40
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
AATATTTTTTT
Found at i:17678255 original size:27 final size:27
Alignment explanation
Indices: 17678225--17678286 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
17678215 CCTATCAGGT
17678225 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
*
17678252 AGGCGCCAATGAAGGTGCCTTATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
17678279 AGGCGCCA
1 AGGCGCCA
17678287 TTACTAGACC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.29, C:0.23, G:0.34, T:0.15
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCATAGAG
Found at i:17678415 original size:23 final size:23
Alignment explanation
Indices: 17678389--17678447 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
17678379 AATAAACACC
17678389 AAAAAAT-TTTTAAAAATAAAAA
1 AAAAAATATTTTAAAAATAAAAA
*
17678411 AAAAAGTATTTTAAAAATAAAAA
1 AAAAAATATTTTAAAAATAAAAA
*
17678434 TAAAAATATATTTA
1 AAAAAATAT-TTTA
17678448 TTGTATTCGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
22 6 0.19
23 22 0.69
24 4 0.12
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (23 bp):
AAAAAATATTTTAAAAATAAAAA
Found at i:17679081 original size:19 final size:19
Alignment explanation
Indices: 17679059--17679096 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
17679049 TATAAATTTA
*
17679059 TTAGTAACTTATTAGTAAT
1 TTAGTAACTTATTACTAAT
*
17679078 TTAGTAATTTATTACTAAT
1 TTAGTAACTTATTACTAAT
17679097 AAATTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (19 bp):
TTAGTAACTTATTACTAAT
Found at i:17679354 original size:27 final size:28
Alignment explanation
Indices: 17679316--17679392 Score: 115
Period size: 27 Copynumber: 2.9 Consensus size: 28
17679306 CCAGCCCGGC
*
17679316 CCATTGGCGCCTCTCAGAAT-GGCACCA
1 CCATTGGCGCCTCCCAGAATAGGCACCA
*
17679343 CCATTGGCGCCTCCCAG-GTAGGCACCA
1 CCATTGGCGCCTCCCAGAATAGGCACCA
17679370 CCATTGGCGCCTCCCAG-ATAGGC
1 CCATTGGCGCCTCCCAGAATAGGC
17679393 GCCAATACTA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 1 0.02
27 45 0.98
ACGTcount: A:0.19, C:0.39, G:0.25, T:0.17
Consensus pattern (28 bp):
CCATTGGCGCCTCCCAGAATAGGCACCA
Found at i:17682392 original size:20 final size:20
Alignment explanation
Indices: 17682367--17682406 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
17682357 CGTAAAATGA
*
17682367 TTTCTGAAAAATGTTTTACT
1 TTTCTGAAAAATGATTTACT
*
17682387 TTTCTGTAAAATGATTTACT
1 TTTCTGAAAAATGATTTACT
17682407 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTCTGAAAAATGATTTACT
Found at i:17682396 original size:34 final size:34
Alignment explanation
Indices: 17682353--17682418 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
17682343 AGTAAAATAT
*
17682353 TTTTCGTAAAATGATTT-CTGAAAAATGTTTTAC
1 TTTTCGTAAAATGATTTACTGAAAAATATTTTAC
*
17682386 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTC-GTAAAATGATTTACTGAAAAATATTTT
17682419 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.41
35 12 0.41
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (34 bp):
TTTTCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:17683947 original size:14 final size:14
Alignment explanation
Indices: 17683925--17683957 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
17683915 ATTGTTTTGC
*
17683925 TATTATATTGTTAT
1 TATTTTATTGTTAT
17683939 TATTTTATTGTTAT
1 TATTTTATTGTTAT
17683953 TATTT
1 TATTT
17683958 GGATATTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (14 bp):
TATTTTATTGTTAT
Found at i:17688070 original size:21 final size:21
Alignment explanation
Indices: 17688046--17688119 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
17688036 ATCTTATATT
17688046 TTTTTTAATAATTTATATAAA
1 TTTTTTAATAATTTATATAAA
* *
17688067 TTTTTTTATAATTT-TCTAAAA
1 TTTTTTAATAATTTATAT-AAA
*
17688088 TTTTTATAATGATTTA-AT-AA
1 TTTTT-TAATAATTTATATAAA
*
17688108 -TTTCTAATAATT
1 TTTTTTAATAATT
17688120 AAAAAAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
18 7 0.16
19 3 0.07
20 4 0.09
21 21 0.49
22 8 0.19
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (21 bp):
TTTTTTAATAATTTATATAAA
Found at i:17688073 original size:22 final size:22
Alignment explanation
Indices: 17688045--17688107 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
17688035 AATCTTATAT
17688045 TTTTTTTAATAATTTATATAAA
1 TTTTTTTAATAATTTATATAAA
*
17688067 TTTTTTT-ATAATTT-TCTAAAA
1 TTTTTTTAATAATTTATAT-AAA
* *
17688088 TTTTTATAATGATTTA-ATAA
1 TTTTTTTAATAATTTATATAA
17688108 TTTCTAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
20 2 0.06
21 18 0.53
22 14 0.41
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTTTTTAATAATTTATATAAA
Found at i:17688423 original size:20 final size:20
Alignment explanation
Indices: 17688400--17688459 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
17688390 TTTTTTATTT
* *
17688400 TTTTTATAATTTTTTAATAA
1 TTTTAATAATTCTTTAATAA
*
17688420 TTTTCAA-AA-ACTTTAATAA
1 TTTT-AATAATTCTTTAATAA
*
17688439 GTTTAATAATTCTTTAATAA
1 TTTTAATAATTCTTTAATAA
17688459 T
1 T
17688460 GTTCTTTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
18 2 0.06
19 13 0.42
20 15 0.48
21 1 0.03
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (20 bp):
TTTTAATAATTCTTTAATAA
Found at i:17688537 original size:19 final size:18
Alignment explanation
Indices: 17688487--17688541 Score: 62
Period size: 16 Copynumber: 3.2 Consensus size: 18
17688477 TTAATATTTT
17688487 TATATA-ATTTTCTAT-A
1 TATATATATTTTCTATAA
*
17688503 TATATATATATT-TATAA
1 TATATATATTTTCTATAA
*
17688520 TATTTCATATTTTCTATAA
1 TATAT-ATATTTTCTATAA
17688539 TAT
1 TAT
17688542 GTTGATAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
16 9 0.28
17 9 0.28
18 6 0.19
19 8 0.25
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATATATTTTCTATAA
Found at i:17689113 original size:24 final size:24
Alignment explanation
Indices: 17689076--17689142 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 24
17689066 TTTTCTTATC
* * *
17689076 ATTGTTTAGATACTGTTGACAAGT
1 ATTGTTTGGGTACTGTTCACAAGT
*
17689100 ATTGTTTGGGTACTATTCACAAGT
1 ATTGTTTGGGTACTGTTCACAAGT
17689124 ATTGTTTGGGTACTGTTCA
1 ATTGTTTGGGTACTGTTCA
17689143 ACATTGTTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.24, C:0.10, G:0.22, T:0.43
Consensus pattern (24 bp):
ATTGTTTGGGTACTGTTCACAAGT
Found at i:17689150 original size:21 final size:23
Alignment explanation
Indices: 17689075--17689161 Score: 79
Period size: 24 Copynumber: 3.8 Consensus size: 23
17689065 TTTTTCTTAT
* * *
17689075 CATTGTTTAGATACTGTTGACAAG
1 CATTGTTTGGGTACTATT-ACAAG
*
17689099 TATTGTTTGGGTACTATTCACAAG
1 CATTGTTTGGGTACTATT-ACAAG
* *
17689123 TATTGTTTGGGTACTGTT-CAA-
1 CATTGTTTGGGTACTATTACAAG
*
17689144 CATTGTTTGAGTACTATT
1 CATTGTTTGGGTACTATT
17689162 TTTGGAAATT
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
21 15 0.28
22 3 0.06
24 36 0.67
ACGTcount: A:0.24, C:0.11, G:0.21, T:0.44
Consensus pattern (23 bp):
CATTGTTTGGGTACTATTACAAG
Found at i:17692031 original size:19 final size:18
Alignment explanation
Indices: 17692009--17692073 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 18
17691999 ATAATTAAGA
17692009 TTAACTTAATTAAACTAGT
1 TTAA-TTAATTAAACTAGT
* *
17692028 TTAATTAAAGTAAAAC-AGA
1 TTAATT-AA-TTAAACTAGT
17692047 TTAACTTAATTAAACTAGT
1 TTAA-TTAATTAAACTAGT
17692066 TTAATTAA
1 TTAATTAA
17692074 AGTAAAACAT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
18 11 0.29
19 20 0.53
20 7 0.18
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (18 bp):
TTAATTAATTAAACTAGT
Found at i:17692050 original size:38 final size:38
Alignment explanation
Indices: 17692006--17692082 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
17691996 TAAATAATTA
17692006 AGATTAACTTAATTAAACTAGTTTAATTAAAGTAAAAC
1 AGATTAACTTAATTAAACTAGTTTAATTAAAGTAAAAC
17692044 AGATTAACTTAATTAAACTAGTTTAATTAAAGTAAAAC
1 AGATTAACTTAATTAAACTAGTTTAATTAAAGTAAAAC
17692082 A
1 A
17692083 TAATATAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.34
Consensus pattern (38 bp):
AGATTAACTTAATTAAACTAGTTTAATTAAAGTAAAAC
Found at i:17692079 original size:19 final size:19
Alignment explanation
Indices: 17692019--17692079 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
17692009 TTAACTTAAT
17692019 TAAACTAGTTTAATTAAAG
1 TAAACTAGTTTAATTAAAG
* *
17692038 TAAAAC-AGATTAACTT-AAT
1 T-AAACTAGTTTAA-TTAAAG
17692057 TAAACTAGTTTAATTAAAG
1 TAAACTAGTTTAATTAAAG
17692076 TAAA
1 TAAA
17692080 ACATAATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 6 0.18
19 22 0.65
20 6 0.18
ACGTcount: A:0.51, C:0.07, G:0.08, T:0.34
Consensus pattern (19 bp):
TAAACTAGTTTAATTAAAG
Found at i:17693110 original size:23 final size:23
Alignment explanation
Indices: 17693073--17693323 Score: 279
Period size: 23 Copynumber: 10.7 Consensus size: 23
17693063 TCTACCCTAT
*
17693073 TTGGACAGC-TCTTATACATCAAA
1 TTGGACAGCAT-TTATACACCAAA
* *
17693096 TCGGACAGCATTTATACACCCAA
1 TTGGACAGCATTTATACACCAAA
*
17693119 TTGGACAGCATATATATATACCAAA
1 TTGGACAGCAT-T-TATACACCAAA
* *
17693144 GTGGATAGCATTTATACACCAAA
1 TTGGACAGCATTTATACACCAAA
* *
17693167 TTGGAGAGCATTTATACACCCAA
1 TTGGACAGCATTTATACACCAAA
* * *
17693190 TTGGATAGCATATATATATACTAAA
1 TTGGACAGCAT-T-TATACACCAAA
* *
17693215 TTGGGCAGCATATATACACCAAA
1 TTGGACAGCATTTATACACCAAA
*
17693238 TTGGACAACATTTATACACCAAA
1 TTGGACAGCATTTATACACCAAA
17693261 TTGGACAGCATTTTATACACCAAA
1 TTGGACAGCA-TTTATACACCAAA
* *
17693285 TTGAACAGCATATATACACCAAA
1 TTGGACAGCATTTATACACCAAA
* *
17693308 TTGGACAACATATATA
1 TTGGACAGCATTTATA
17693324 TATATATACC
Statistics
Matches: 193, Mismatches: 29, Indels: 12
0.82 0.12 0.05
Matches are distributed among these distances:
23 132 0.68
24 26 0.13
25 35 0.18
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (23 bp):
TTGGACAGCATTTATACACCAAA
Found at i:17693158 original size:48 final size:48
Alignment explanation
Indices: 17693073--17693325 Score: 277
Period size: 48 Copynumber: 5.4 Consensus size: 48
17693063 TCTACCCTAT
* * * *
17693073 TTGGACAGC-TCT-TATACATCAAATCGGACAGCATTTATACACCCAA
1 TTGGACAGCATATATATACACCAAATTGGACAGCATTTATACACCAAA
* * *
17693119 TTGGACAGCATATATATATACCAAAGTGGATAGCATTTATACACCAAA
1 TTGGACAGCATATATATACACCAAATTGGACAGCATTTATACACCAAA
* * * * *
17693167 TTGGAGAGCAT-T-TATACACCCAATTGGATAGCATATATATATACTAAA
1 TTGGACAGCATATATATACACCAAATTGGACAGCAT-T-TATACACCAAA
* *
17693215 TTGGGCAGC--ATATATACACCAAATTGGACAACATTTATACACCAAA
1 TTGGACAGCATATATATACACCAAATTGGACAGCATTTATACACCAAA
* * *
17693261 TTGGACAGCAT-TTTATACACCAAATTGAACAGCATATATACACCAAA
1 TTGGACAGCATATATATACACCAAATTGGACAGCATTTATACACCAAA
*
17693308 TTGGACAACATATATATA
1 TTGGACAGCATATATATA
17693326 TATATACCCA
Statistics
Matches: 171, Mismatches: 27, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
46 45 0.26
47 48 0.28
48 78 0.46
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.27
Consensus pattern (48 bp):
TTGGACAGCATATATATACACCAAATTGGACAGCATTTATACACCAAA
Found at i:17693200 original size:71 final size:71
Alignment explanation
Indices: 17693085--17693323 Score: 327
Period size: 71 Copynumber: 3.4 Consensus size: 71
17693075 GGACAGCTCT
* * * *
17693085 TATACATCAAATCGGACAGCATTTATACACCCAATTGGACAGCATATATATATACCAAAGTGGAT
1 TATACACCAAATTGGACAGCATTTATACACCCAATTGGACAGCATATATATATACCAAATTGGAC
*
17693150 AGCATT
66 AGCATA
* * * *
17693156 TATACACCAAATTGGAGAGCATTTATACACCCAATTGGATAGCATATATATATACTAAATTGGGC
1 TATACACCAAATTGGACAGCATTTATACACCCAATTGGACAGCATATATATATACCAAATTGGAC
17693221 AGCATA
66 AGCATA
* * * * *
17693227 TATACACCAAATTGGACAACATTTATACACCAAATTGGACAGCAT-TTTATACACCAAATTGAAC
1 TATACACCAAATTGGACAGCATTTATACACCCAATTGGACAGCATATATATATACCAAATTGGAC
17693291 AGCATA
66 AGCATA
* *
17693297 TATACACCAAATTGGACAACATATATA
1 TATACACCAAATTGGACAGCATTTATA
17693324 TATATATACC
Statistics
Matches: 149, Mismatches: 19, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
70 46 0.31
71 103 0.69
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (71 bp):
TATACACCAAATTGGACAGCATTTATACACCCAATTGGACAGCATATATATATACCAAATTGGAC
AGCATA
Found at i:17694402 original size:43 final size:42
Alignment explanation
Indices: 17694304--17694434 Score: 108
Period size: 43 Copynumber: 3.0 Consensus size: 42
17694294 ATATCGTACA
* *
17694304 ATGCCAACGTCCCAGACGTAGTCTTACATGTAATCACATAACG
1 ATGCCAACGTCCCAGAC-TAGTCTTACACGTAAACACATAACG
**
17694347 ATGCC-ACTGTCCCAGA-TAGGGTCTTACACGTAAACACA-AGTTG
1 ATGCCAAC-GTCCCAGACTA--GTCTTACACGTAAACACATA-ACG
*
17694390 ATGCCAACGTCCCCCAGACGTGGTCTTACACG-ATAACACATAACG
1 ATGCCAACGT--CCCAGAC-TAGTCTTACACGTA-AACACATAACG
17694435 GAATCCTATG
Statistics
Matches: 70, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
41 2 0.03
42 3 0.04
43 37 0.53
44 3 0.04
45 23 0.33
46 1 0.01
47 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.21
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACTAGTCTTACACGTAAACACATAACG
Found at i:17696509 original size:14 final size:15
Alignment explanation
Indices: 17696490--17696518 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17696480 GGATTTTTAT
17696490 GGTAT-AATGTGAAA
1 GGTATAAATGTGAAA
17696504 GGTATAAATGTGAAA
1 GGTATAAATGTGAAA
17696519 TTTCATGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.45, C:0.00, G:0.28, T:0.28
Consensus pattern (15 bp):
GGTATAAATGTGAAA
Found at i:17696594 original size:44 final size:44
Alignment explanation
Indices: 17696531--17696621 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
17696521 TCATGTATGG
17696531 TTTAAAGTTGGTGTTTGGCAAGCAACTTGATTTGGTTAACTCTC
1 TTTAAAGTTGGTGTTTGGCAAGCAACTTGATTTGGTTAACTCTC
17696575 TTTAAAGTTGGTGTTTGGCAAGCAACTTGATTTGGTTAACTCTC
1 TTTAAAGTTGGTGTTTGGCAAGCAACTTGATTTGGTTAACTCTC
17696619 TTT
1 TTT
17696622 CTATGTTGAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.43
Consensus pattern (44 bp):
TTTAAAGTTGGTGTTTGGCAAGCAACTTGATTTGGTTAACTCTC
Found at i:17698448 original size:16 final size:16
Alignment explanation
Indices: 17698427--17698460 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
17698417 CCAATATCCA
*
17698427 ATTATCATATTTGCAC
1 ATTATCATATTTACAC
17698443 ATTATCATATTTACAC
1 ATTATCATATTTACAC
17698459 AT
1 AT
17698461 ATATATTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.03, T:0.44
Consensus pattern (16 bp):
ATTATCATATTTACAC
Found at i:17702953 original size:22 final size:22
Alignment explanation
Indices: 17702919--17702963 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
17702909 TAAAAATCCT
*
17702919 AGAAAAGTGTAGAGAAAAACTAA
1 AGAAAACTGTAGAG-AAAACTAA
17702942 AGAAAACT-TAGAGAAAACTAA
1 AGAAAACTGTAGAGAAAACTAA
17702963 A
1 A
17702964 CCTAAAACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 5 0.24
23 7 0.33
ACGTcount: A:0.62, C:0.07, G:0.18, T:0.13
Consensus pattern (22 bp):
AGAAAACTGTAGAGAAAACTAA
Found at i:17706373 original size:32 final size:30
Alignment explanation
Indices: 17706321--17706379 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 30
17706311 ATGTTTTCTT
*
17706321 TTTTTGATATAAATATTTATTGTTATTTTC
1 TTTTTCATATAAATATTTATTGTTATTTTC
*
17706351 TTTTTCATAGTAATTATGTTATTGTTATT
1 TTTTTCATA-TAAATAT-TTATTGTTATT
17706380 GGGTATTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 8 0.32
31 6 0.24
32 11 0.44
ACGTcount: A:0.25, C:0.03, G:0.08, T:0.63
Consensus pattern (30 bp):
TTTTTCATATAAATATTTATTGTTATTTTC
Found at i:17709193 original size:15 final size:16
Alignment explanation
Indices: 17709173--17709204 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
17709163 GATATCACCG
17709173 ACAAAAAAAAA-TTAT
1 ACAAAAAAAAAGTTAT
17709188 ACAAAAAAAAAGTTAT
1 ACAAAAAAAAAGTTAT
17709204 A
1 A
17709205 AGGATATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.72, C:0.06, G:0.03, T:0.19
Consensus pattern (16 bp):
ACAAAAAAAAAGTTAT
Found at i:17711625 original size:28 final size:28
Alignment explanation
Indices: 17711593--17711650 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
17711583 TTACTGCTGT
*
17711593 TTTATTAGCTTTTTTTGTTTATATCATG
1 TTTATTAGCTTTTGTTGTTTATATCATG
17711621 TTTATTAGCTTTTGTTGTTTATATCATG
1 TTTATTAGCTTTTGTTGTTTATATCATG
17711649 TT
1 TT
17711651 GGTTGGGCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.17, C:0.07, G:0.12, T:0.64
Consensus pattern (28 bp):
TTTATTAGCTTTTGTTGTTTATATCATG
Found at i:17717890 original size:16 final size:16
Alignment explanation
Indices: 17717869--17717904 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
17717859 TTTGGTTCGC
17717869 TGTATTAGATTAGAGG
1 TGTATTAGATTAGAGG
*
17717885 TGTATTGGATTAGAGG
1 TGTATTAGATTAGAGG
17717901 TGTA
1 TGTA
17717905 ATAGCAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.33, T:0.39
Consensus pattern (16 bp):
TGTATTAGATTAGAGG
Found at i:17719316 original size:25 final size:25
Alignment explanation
Indices: 17719250--17719428 Score: 208
Period size: 25 Copynumber: 7.2 Consensus size: 25
17719240 TTTAAATTTA
* * *
17719250 TTTATTAAAATATTAAATTTCTTGATT
1 TTTAATAAAATATTAAAGTCCTT-A-T
17719277 TTTAATAAAATATTAAAGTCCTTAT
1 TTTAATAAAATATTAAAGTCCTTAT
* *
17719302 TTTAAT-TATTGATT--AGTCCTTAT
1 TTTAATAAAAT-ATTAAAGTCCTTAT
17719325 TTTAATAAAATATTAAAGTCCTTAT
1 TTTAATAAAATATTAAAGTCCTTAT
* *
17719350 TTTAAT-TATTGATT--AGTCCTTAT
1 TTTAATAAAAT-ATTAAAGTCCTTAT
17719373 TTTAATAAAATATTAAAGTCCTTAT
1 TTTAATAAAATATTAAAGTCCTTAT
*
17719398 TTTAATAAAATATTAAAGTCCTTAC
1 TTTAATAAAATATTAAAGTCCTTAT
17719423 TTTAAT
1 TTTAAT
17719429 TATTGATGTA
Statistics
Matches: 132, Mismatches: 12, Indels: 18
0.81 0.07 0.11
Matches are distributed among these distances:
23 36 0.27
24 8 0.06
25 67 0.51
26 1 0.01
27 20 0.15
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (25 bp):
TTTAATAAAATATTAAAGTCCTTAT
Found at i:17719328 original size:48 final size:48
Alignment explanation
Indices: 17719276--17719403 Score: 256
Period size: 48 Copynumber: 2.7 Consensus size: 48
17719266 ATTTCTTGAT
17719276 TTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTTA
1 TTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTTA
17719324 TTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTTA
1 TTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTTA
17719372 TTTTAATAAAATATTAAAGTCCTTATTTTAAT
1 TTTTAATAAAATATTAAAGTCCTTATTTTAAT
17719404 AAAATATTAA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 80 1.00
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (48 bp):
TTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTTA
Found at i:17719355 original size:73 final size:72
Alignment explanation
Indices: 17719250--17719428 Score: 202
Period size: 73 Copynumber: 2.4 Consensus size: 72
17719240 TTTAAATTTA
* * * * *
17719250 TTTATTAAAATATTAAATTTCTTGATTTTTAATAAAAT-ATTAAAGTCCTTATTTTAAT-TATTG
1 TTTAATAAAATATTAAAGTCCTT-A-TTTTAAT-AAATGATT--AGTCCTTATTTTAATAAAAT-
17719313 ATT-AGTCCTTAT
60 ATTAAGTCCTTAT
* *
17719325 TTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTTATTTTAATAAAATATTAAA
1 TTTAATAAAATATTAAAGTCCTTATTTTAATAAATGATTAGTCCTTATTTTAATAAAATATT-AA
17719390 GTCCTTAT
65 GTCCTTAT
*
17719398 TTTAATAAAATATTAAAGTCCTTACTTTAAT
1 TTTAATAAAATATTAAAGTCCTTATTTTAAT
17719429 TATTGATGTA
Statistics
Matches: 92, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
71 18 0.20
72 4 0.04
73 49 0.53
74 1 0.01
75 20 0.22
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (72 bp):
TTTAATAAAATATTAAAGTCCTTATTTTAATAAATGATTAGTCCTTATTTTAATAAAATATTAAG
TCCTTAT
Found at i:17720400 original size:2 final size:2
Alignment explanation
Indices: 17720393--17720433 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
17720383 TGGCAGCATA
17720393 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17720434 AACATACAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17729450 original size:12 final size:12
Alignment explanation
Indices: 17729433--17729458 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17729423 GACTCCACTT
17729433 GATTTATTAACA
1 GATTTATTAACA
17729445 GATTTATTAACA
1 GATTTATTAACA
17729457 GA
1 GA
17729459 AACCTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (12 bp):
GATTTATTAACA
Found at i:17736565 original size:103 final size:103
Alignment explanation
Indices: 17736382--17736582 Score: 278
Period size: 103 Copynumber: 2.0 Consensus size: 103
17736372 CATAGGTCTT
* ** * *
17736382 ACATCAAACACCTCTTTATAGGGATCAATAGATATTGTGTCAATAGATTGGAAGGAGAATTTTCC
1 ACATCAAACACCCCTCCATAGGGATCAATAGATATTGTGCCAATAGATAGGAAGGAGAATTTTCC
* *
17736447 GAAAGTTATTCAAAGTATTTTCCCATGTCCACCCTTAG
66 AAAAGTCATTCAAAGTATTTTCCCATGTCCACCCTTAG
* *
17736485 ACATCAAACACCCCTCCATAAGGG-TCAATTGATATTGTGCCAATAGATAGGAAGGAGCATTTTC
1 ACATCAAACACCCCTCCAT-AGGGATCAATAGATATTGTGCCAATAGATAGGAAGGAGAATTTTC
* **
17736549 CAAAAGTCATTTAAAGTATTTTGTCATGTCCACC
65 CAAAAGTCATTCAAAGTATTTTCCCATGTCCACC
17736583 AGCAATTCAC
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
103 81 0.95
104 4 0.05
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.30
Consensus pattern (103 bp):
ACATCAAACACCCCTCCATAGGGATCAATAGATATTGTGCCAATAGATAGGAAGGAGAATTTTCC
AAAAGTCATTCAAAGTATTTTCCCATGTCCACCCTTAG
Found at i:17739318 original size:21 final size:21
Alignment explanation
Indices: 17739276--17739318 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
17739266 ATTATACTCT
* *
17739276 ATTTTTAACTATTTATTTTAC
1 ATTTTTAACTATTTACTGTAC
17739297 ATTTTTAACT-TTTAACTGTAC
1 ATTTTTAACTATTT-ACTGTAC
17739318 A
1 A
17739319 ATACTTCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.30, C:0.12, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTTTTAACTATTTACTGTAC
Found at i:17753129 original size:24 final size:24
Alignment explanation
Indices: 17753098--17753229 Score: 239
Period size: 24 Copynumber: 5.5 Consensus size: 24
17753088 ATACGGAACA
17753098 AATA-CAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
17753121 AATATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
* *
17753145 AATATCAAAGAGCACCAATGTGCT
1 AATATCAGAGAGCACCAACGTGCT
17753169 AATATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
17753193 AATATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
17753217 AATATCAGAGAGC
1 AATATCAGAGAGC
17753230 GCGCTAAAGT
Statistics
Matches: 104, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
23 4 0.04
24 100 0.96
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.17
Consensus pattern (24 bp):
AATATCAGAGAGCACCAACGTGCT
Found at i:17754328 original size:12 final size:12
Alignment explanation
Indices: 17754313--17754350 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
17754303 CCCGTTTTGC
17754313 TCTCTGTTTCTT
1 TCTCTGTTTCTT
*
17754325 TCTCTGTTTCTA
1 TCTCTGTTTCTT
17754337 T-TCTG-TTCTT
1 TCTCTGTTTCTT
17754347 TCTC
1 TCTC
17754351 CTTTCTATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 5 0.22
11 6 0.26
12 12 0.52
ACGTcount: A:0.03, C:0.26, G:0.08, T:0.63
Consensus pattern (12 bp):
TCTCTGTTTCTT
Found at i:17754357 original size:21 final size:22
Alignment explanation
Indices: 17754315--17754367 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
17754305 CGTTTTGCTC
*
17754315 TCTGTTTCTTTCTCTGTTTCTAT
1 TCTG-TTCTTTCTCTCTTTCTAT
17754338 TCTGTTCTTTCTC-CTTTCTAT
1 TCTGTTCTTTCTCTCTTTCTAT
17754359 TCT-TTCTTT
1 TCTGTTCTTT
17754368 TGTTGTTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 6 0.21
21 10 0.34
22 9 0.31
23 4 0.14
ACGTcount: A:0.04, C:0.25, G:0.06, T:0.66
Consensus pattern (22 bp):
TCTGTTCTTTCTCTCTTTCTAT
Found at i:17754390 original size:5 final size:5
Alignment explanation
Indices: 17754375--17754420 Score: 60
Period size: 5 Copynumber: 9.2 Consensus size: 5
17754365 TTTTGTTGTT
17754375 ATATAA ATATA ATATA ATATA ATAT- AT-TA ATAATA ATATA ATATA A
1 ATAT-A ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA ATATA A
17754421 AAACATAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
3 1 0.03
4 4 0.11
5 24 0.65
6 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:17754412 original size:19 final size:17
Alignment explanation
Indices: 17754375--17754419 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 17
17754365 TTTTGTTGTT
17754375 ATATAA-ATATAATATA
1 ATATAATATATAATATA
17754391 ATATAATATATTAATAATA
1 ATATAATATA-TAAT-ATA
17754410 ATATAATATA
1 ATATAATATA
17754420 AAAACATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.23
17 3 0.12
18 4 0.15
19 13 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAATATATAATATA
Found at i:17754415 original size:24 final size:23
Alignment explanation
Indices: 17754374--17754420 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
17754364 CTTTTGTTGT
17754374 TATATAAATATAATATAATATAA
1 TATATAAATATAATATAATATAA
*
17754397 TATATTAATAATAATATAATATAA
1 TATATAAAT-ATAATATAATATAA
17754421 AAACATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
TATATAAATATAATATAATATAA
Found at i:17754429 original size:24 final size:24
Alignment explanation
Indices: 17754383--17754429 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
17754373 TTATATAAAT
* *
17754383 ATAATATAATATAATATATTAATA
1 ATAATATAATATAATAAAATAATA
17754407 ATAATATAATATAA-AAACATAAT
1 ATAATATAATATAATAAA-ATAAT
17754430 TATTACTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
ATAATATAATATAATAAAATAATA
Found at i:17760997 original size:20 final size:20
Alignment explanation
Indices: 17760972--17761022 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 20
17760962 ATAAAAAGGT
17760972 AAGGTATCGATACCTTG-GAA
1 AAGGTATCGATACCTTGTG-A
*
17760992 AAGGTA--GATACTTTGTGA
1 AAGGTATCGATACCTTGTGA
*
17761010 CAGGTATCGATAC
1 AAGGTATCGATAC
17761023 ATTTGTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 14 0.54
19 1 0.04
20 11 0.42
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.27
Consensus pattern (20 bp):
AAGGTATCGATACCTTGTGA
Found at i:17764939 original size:7 final size:7
Alignment explanation
Indices: 17764927--17764953 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
17764917 AAACCCTCTA
17764927 CCATCAC
1 CCATCAC
17764934 CCATCAC
1 CCATCAC
17764941 CCATCAC
1 CCATCAC
17764948 CCATCA
1 CCATCA
17764954 TCTTCATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.56, G:0.00, T:0.15
Consensus pattern (7 bp):
CCATCAC
Found at i:17769500 original size:39 final size:39
Alignment explanation
Indices: 17769441--17769518 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
17769431 AGTAGCACCA
* *
17769441 AAAATTTATATCTTTGATTTCTTCTGCAATTAAAATTTG
1 AAAACTTATATATTTGATTTCTTCTGCAATTAAAATTTG
* *
17769480 AAAACTTATATATTTGATTTCTTCTGTAATTAAATTTTG
1 AAAACTTATATATTTGATTTCTTCTGCAATTAAAATTTG
17769519 CAAAGAGAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.33, C:0.09, G:0.08, T:0.50
Consensus pattern (39 bp):
AAAACTTATATATTTGATTTCTTCTGCAATTAAAATTTG
Found at i:17772353 original size:37 final size:39
Alignment explanation
Indices: 17772310--17772388 Score: 108
Period size: 42 Copynumber: 2.0 Consensus size: 39
17772300 TTCAATTATC
17772310 CTTGTTTG-C-TTACTTTAAAATAGTATAAAAAATTAAA
1 CTTGTTTGTCTTTACTTTAAAATAGTATAAAAAATTAAA
*
17772347 CTTGTTTGTTCACTTTACTTTAAAATAGTATAAAAGATTAAA
1 CTTGTTTG-T--CTTTACTTTAAAATAGTATAAAAAATTAAA
17772389 TTGATTGATT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
37 8 0.22
41 1 0.03
42 27 0.75
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.42
Consensus pattern (39 bp):
CTTGTTTGTCTTTACTTTAAAATAGTATAAAAAATTAAA
Found at i:17772412 original size:42 final size:42
Alignment explanation
Indices: 17772319--17772403 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 42
17772309 CCTTGTTTGC
* *
17772319 TTACTTTAAAATAGTATAAAAAATTAAACTTGTTTGTTCACT
1 TTACTTTAAAATAGTATAAAAAATTAAACTTGATTGTTCAAT
*
17772361 TTACTTTAAAATAGTATAAAAGATTAAA-TTGATTGATT-AAT
1 TTACTTTAAAATAGTATAAAAAATTAAACTTGATTG-TTCAAT
17772402 TT
1 TT
17772404 TTTATTAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
41 10 0.26
42 29 0.74
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (42 bp):
TTACTTTAAAATAGTATAAAAAATTAAACTTGATTGTTCAAT
Found at i:17772535 original size:38 final size:38
Alignment explanation
Indices: 17772484--17772559 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
17772474 TACTTATACC
*
17772484 GAACAAATTTTATTAAAGATTTCATTATAGTATAAATA
1 GAACAAAATTTATTAAAGATTTCATTATAGTATAAATA
17772522 GAACAAAATTTATTAAAGATTTCATTATAGTATAAATA
1 GAACAAAATTTATTAAAGATTTCATTATAGTATAAATA
17772560 AAAATAAGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (38 bp):
GAACAAAATTTATTAAAGATTTCATTATAGTATAAATA
Found at i:17773977 original size:15 final size:17
Alignment explanation
Indices: 17773948--17773986 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
17773938 TTAATGTAAC
*
17773948 ATTTATTTTTCATATCA
1 ATTTATTTTTCATATAA
17773965 ATTT-TTTTT-ATATAA
1 ATTTATTTTTCATATAA
17773980 ATTTATT
1 ATTTATT
17773987 ACACAATGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 9 0.45
16 7 0.35
17 4 0.20
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTATTTTTCATATAA
Found at i:17774971 original size:17 final size:19
Alignment explanation
Indices: 17774935--17774973 Score: 55
Period size: 17 Copynumber: 2.1 Consensus size: 19
17774925 AAGAGATTCG
17774935 TTTATTTTTATATGAAATAA
1 TTTATTTTTATA-GAAATAA
17774955 TTTA-TTTTATA-AAATAA
1 TTTATTTTTATAGAAATAA
17774972 TT
1 TT
17774974 ATTGTTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
19 7 0.37
20 4 0.21
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
TTTATTTTTATAGAAATAA
Found at i:17775960 original size:29 final size:27
Alignment explanation
Indices: 17775919--17775973 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 27
17775909 TATTAAACTT
17775919 ACATATTTATA-TTTAATAACATAATTA
1 ACATATTTATATTTTAATAA-ATAATTA
17775946 ACATAATTTATTATTTTAATAAATAATT
1 ACAT-ATTTA-TATTTTAATAAATAATT
17775974 TAATATTGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 4 0.16
28 5 0.20
29 8 0.32
30 8 0.32
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (27 bp):
ACATATTTATATTTTAATAAATAATTA
Found at i:17778999 original size:44 final size:44
Alignment explanation
Indices: 17778949--17779039 Score: 139
Period size: 44 Copynumber: 2.1 Consensus size: 44
17778939 AATTCTGTTT
17778949 TTAGTTTACCACTTAAACTTTAATTAGTGTA-AGTTATTTTAATA
1 TTAGTTTACCACTTAAACTTTAATTAGTGTAGA-TTATTTTAATA
* * *
17778993 TTAGTTTTCCACTTAAATTTTGATTAGTGTAGATTATTTTAATA
1 TTAGTTTACCACTTAAACTTTAATTAGTGTAGATTATTTTAATA
17779037 TTA
1 TTA
17779040 TTTGACCTAC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 42 0.98
45 1 0.02
ACGTcount: A:0.32, C:0.08, G:0.10, T:0.51
Consensus pattern (44 bp):
TTAGTTTACCACTTAAACTTTAATTAGTGTAGATTATTTTAATA
Found at i:17781996 original size:16 final size:17
Alignment explanation
Indices: 17781961--17781998 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
17781951 TTAGGATATG
17781961 TGGGTTTTATTTTGAAT
1 TGGGTTTTATTTTGAAT
17781978 TGGGATTTTA-TTT-AAT
1 TGGG-TTTTATTTTGAAT
17781994 TGGGT
1 TGGGT
17781999 CAGACATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 1 0.05
16 7 0.35
17 7 0.35
18 5 0.25
ACGTcount: A:0.18, C:0.00, G:0.26, T:0.55
Consensus pattern (17 bp):
TGGGTTTTATTTTGAAT
Found at i:17791683 original size:29 final size:30
Alignment explanation
Indices: 17791624--17791681 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
17791614 TCCGAGCCTT
* *
17791624 GGGGCAAAAATGTAATTATGTAAACGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
17791654 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
17791682 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.40, C:0.05, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:17791912 original size:13 final size:13
Alignment explanation
Indices: 17791894--17791924 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
17791884 TTCCAGCAAC
17791894 TATGAATTTATTT
1 TATGAATTTATTT
17791907 TATGAATTTATTT
1 TATGAATTTATTT
*
17791920 GATGA
1 TATGA
17791925 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:17793847 original size:22 final size:22
Alignment explanation
Indices: 17793815--17793860 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
17793805 TGGCACACCT
17793815 TAATCTGGAGTAGATGACGAAC
1 TAATCTGGAGTAGATGACGAAC
*
17793837 TAATCTTGAGTAGATGACGAAC
1 TAATCTGGAGTAGATGACGAAC
17793859 TA
1 TA
17793861 TGTATGTGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (22 bp):
TAATCTGGAGTAGATGACGAAC
Found at i:17797224 original size:13 final size:13
Alignment explanation
Indices: 17797203--17797233 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
17797193 GCTTAGATCA
*
17797203 TCATCAAATAAAT
1 TCATAAAATAAAT
17797216 TCATAAAATAAAT
1 TCATAAAATAAAT
17797229 TCATA
1 TCATA
17797234 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:17798541 original size:56 final size:50
Alignment explanation
Indices: 17798323--17798571 Score: 327
Period size: 50 Copynumber: 4.8 Consensus size: 50
17798313 GATAATAACA
* ** * *
17798323 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
17798374 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
17798424 TGCCAATGCCATGACCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
17798474 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATC-T-CGG
*
17798529 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
17798572 TTACCCAAAT
Statistics
Matches: 175, Mismatches: 17, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
50 96 0.55
51 33 0.19
53 3 0.02
54 1 0.01
55 2 0.01
56 40 0.23
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:17798687 original size:13 final size:13
Alignment explanation
Indices: 17798666--17798697 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
17798656 GCTTGGATCA
*
17798666 TCATCAAATAAAT
1 TCATAAAATAAAT
17798679 TCATAAAATAAAT
1 TCATAAAATAAAT
17798692 TCATAA
1 TCATAA
17798698 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:17798944 original size:30 final size:30
Alignment explanation
Indices: 17798909--17798966 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
17798899 CCTCGACTCT
*
17798909 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
17798939 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
17798967 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:17803859 original size:19 final size:19
Alignment explanation
Indices: 17803823--17803861 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
17803813 CTTTCATGCC
* **
17803823 TTGGTGTGTTGGTTGGATA
1 TTGGTGTGTTAGAGGGATA
17803842 TTGGTGTGTTAGAGGGATA
1 TTGGTGTGTTAGAGGGATA
17803861 T
1 T
17803862 GATTGATGCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.41, T:0.44
Consensus pattern (19 bp):
TTGGTGTGTTAGAGGGATA
Found at i:17811019 original size:44 final size:44
Alignment explanation
Indices: 17810905--17811430 Score: 350
Period size: 44 Copynumber: 11.7 Consensus size: 44
17810895 TCATTCTAAC
* * * *
17810905 CCACTGCAACTTCAGGGATATAGGAGTTGTAG-TCTCAATCTACG
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGAT-TCAATCTACT
* * * * * *
17810949 CCGCTGTAAATTCAAGGG-TATGAGATTTGTATATTCAATCTACT
1 CCACTGCAACTTC-AGGGAGATAAGATTTGTAGATTCAATCTACT
* * *
17810993 CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTGTAGCTTTAGTCTATT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTA----G-A--TTCAATCTACT
* * * *
17811044 CCACTACAACTTCAGGGAAATAAGACTTGCTATGGTAGATTTAATCCGAC-
1 CCACTGCAACTTCAGGGAGATAAGA--T--T-T-GTAGATTCAAT-CTACT
* * * *
17811094 CTACTGCAACTTCA--GAGATACTAGATTTGTCGCTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATA--AGATTTGTAGATTCAATCTACT
* * * *
17811138 CCATTGCAATTTCAGGGAGATAAGATTTGTAGCTTTAATCTA-T
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGATTCAATCTACT
* ** *
17811181 CCACTGCAATTTCACAGAGATAAGATTTGTAGCTTCAATCTAC-
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGATTCAATCTACT
* * ** *
17811224 CCTACTGCAACTTTAGAGAGATAAGATTTGCTATTTTCAATCTGCT
1 CC-ACTGCAACTTCAGGGAGATAAGATTTG-TAGATTCAATCTACT
* *
17811270 CCACTGCAACTTCAGGGAGATAGGATTTGTA-ACTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGA-TTCAATCTACT
* * * * *
17811314 CTACTGTAACTTTAGAGAGATAAGATTCGTA-ATTTCAATCTACT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGA-TTCAATCTACT
* * * * *
17811358 CCACTGCAACTTCAGGGAGATAAGATTTGTGGCTTTAATTTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGATTCAATCTACT
* * *
17811402 TCACTACAACTTCAGGGAGATAAAATTTG
1 CCACTGCAACTTCAGGGAGATAAGATTTG
17811431 CCACGATAAC
Statistics
Matches: 383, Mismatches: 71, Indels: 56
0.75 0.14 0.11
Matches are distributed among these distances:
43 47 0.12
44 218 0.57
45 41 0.11
46 9 0.02
48 6 0.02
49 1 0.00
50 20 0.05
51 33 0.09
52 1 0.00
53 2 0.01
55 1 0.00
56 1 0.00
57 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (44 bp):
CCACTGCAACTTCAGGGAGATAAGATTTGTAGATTCAATCTACT
Found at i:17811285 original size:132 final size:131
Alignment explanation
Indices: 17810971--17811430 Score: 401
Period size: 132 Copynumber: 3.4 Consensus size: 131
17810961 CAAGGGTATG
* *
17810971 AGATTTGTATATTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTGTAGCTTT
1 AGATTTGTATTTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTT-TA-----
* * * * * *
17811036 AGTCTATTCCACTACAACTTCAGGGAAATAAGACTTGCTATGGTAGATTTAATCCGA-CCTACTG
60 A-TCTA-TCCACTGCAATTTCAGAGAGATAAGA--T--T-T-GTAGATTCAAT-CTACCCTACTG
*
17811100 CAACTTCAGAGATACT-
116 CAACTTCAGAGAGA-TA
*** * *
17811116 AGATTTGTCGCTTCAATCTGCTCCATTGCAATTTCAGGGAGATAAGATTTGTAGCTTTAATCTAT
1 AGATTTGTATTTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTAT
* * *
17811181 CCACTGCAATTTCACAGAGATAAGATTTGTAGCTTCAATCTACCCTACTGCAACTTTAGAGAGAT
66 CCACTGCAATTTCAGAGAGATAAGATTTGTAGATTCAATCTACCCTACTGCAACTTCAGAGAGAT
17811246 A
131 A
* * *
17811247 AGATTTGCTATTTTCAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTTGTAACTTCAATCTG
1 AGATTTG-TATTTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCT-
* * * * *
17811312 CTCTACTGTAACTTT-AGAGAGATAAGATTCGTA-ATTTCAATCTACTCC-ACTGCAACTTCAGG
64 ATCCACTGCAA-TTTCAGAGAGATAAGATTTGTAGA-TTCAATCTAC-CCTACTGCAACTTCAGA
17811374 GAGATA
126 GAGATA
** * * * *
17811380 AGATTTGTGGCTTT-AATTTGCTTCACTACAACTTCAGGGAGATAAAATTTG
1 AGATTTGT-ATTTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG
17811431 CCACGATAAC
Statistics
Matches: 268, Mismatches: 39, Indels: 29
0.80 0.12 0.09
Matches are distributed among these distances:
130 3 0.01
131 35 0.13
132 82 0.31
133 63 0.24
134 5 0.02
135 1 0.00
137 21 0.08
138 4 0.01
139 1 0.00
144 2 0.01
145 51 0.19
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (131 bp):
AGATTTGTATTTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTAT
CCACTGCAATTTCAGAGAGATAAGATTTGTAGATTCAATCTACCCTACTGCAACTTCAGAGAGAT
A
Found at i:17811306 original size:89 final size:87
Alignment explanation
Indices: 17811096--17811392 Score: 341
Period size: 89 Copynumber: 3.4 Consensus size: 87
17811086 AATCCGACCT
* * * *
17811096 ACTGCAACTTCAGAGATACT-AGATTTGTCGCTTCAATCTGCTCC-ATTGCAA-TTTCAGGGAGA
1 ACTGCAACTTCAGAGAGA-TAAGATTTGTAGCTTCAATCTGC-CCTACTGCAACTTT-AGAGAGA
* *
17811158 TAAGATTTGTAGCTTT-AATCTATCC
63 TAAGATTTGTA-ATTTCAATCTCTCC
* * *
17811183 ACTGCAATTTCACAGAGATAAGATTTGTAGCTTCAATCTACCCTACTGCAACTTTAGAGAGATAA
1 ACTGCAACTTCAGAGAGATAAGATTTGTAGCTTCAATCTGCCCTACTGCAACTTTAGAGAGATAA
*
17811248 GATTTGCTATTTTCAATCTGCTCC
66 GATTTG-TAATTTCAATCT-CTCC
* * * * *
17811272 ACTGCAACTTCAGGGAGATAGGATTTGTAACTTCAATCTGCTCTACTGTAACTTTAGAGAGATAA
1 ACTGCAACTTCAGAGAGATAAGATTTGTAGCTTCAATCTGCCCTACTGCAACTTTAGAGAGATAA
*
17811337 GATTCGTAATTTCAATCTACTCC
66 GATTTGTAATTTCAATCT-CTCC
* *
17811360 ACTGCAACTTCAGGGAGATAAGATTTGTGGCTT
1 ACTGCAACTTCAGAGAGATAAGATTTGTAGCTT
17811393 TAATTTGCTT
Statistics
Matches: 181, Mismatches: 23, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
86 3 0.02
87 58 0.32
88 55 0.30
89 65 0.36
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (87 bp):
ACTGCAACTTCAGAGAGATAAGATTTGTAGCTTCAATCTGCCCTACTGCAACTTTAGAGAGATAA
GATTTGTAATTTCAATCTCTCC
Found at i:17819218 original size:19 final size:20
Alignment explanation
Indices: 17819196--17819248 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
17819186 GGATCTTTTC
*
17819196 ATGAAATTTAATGCAGATG-
1 ATGAAATGTAATGCAGATGA
*
17819215 ATGAAATGTAATGCCGATGA
1 ATGAAATGTAATGCAGATGA
17819235 ATGAAATG-AATGCA
1 ATGAAATGTAATGCA
17819249 AAAAGAGGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 22 0.73
20 8 0.27
ACGTcount: A:0.43, C:0.08, G:0.23, T:0.26
Consensus pattern (20 bp):
ATGAAATGTAATGCAGATGA
Found at i:17825162 original size:6 final size:6
Alignment explanation
Indices: 17825151--17825237 Score: 174
Period size: 6 Copynumber: 14.5 Consensus size: 6
17825141 TCTCAACACC
17825151 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
17825199 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATA
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATA
17825238 AAGGGCCAAA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 81 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:17825447 original size:6 final size:6
Alignment explanation
Indices: 17825436--17825745 Score: 539
Period size: 6 Copynumber: 51.7 Consensus size: 6
17825426 CACACACATG
17825436 TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA
1 TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA
*
17825484 TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA CATAGA
1 TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA
* * * * *
17825532 CATAGA CATAGA CATAGA CATAGA CATAGA TATAGA TATAGA TATAGA
1 TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA
17825580 TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA
1 TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA
* *
17825628 TATAGA TATAGA TATAGA TATAGA TATAGA TAAATA TATAGA TATAGA
1 TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA
*
17825676 TATAGA TATAGC TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA
1 TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA
17825724 TATAGA TATAGA TATAGA TATA
1 TATAGA TATAGA TATAGA TATA
17825746 TCATATAAGG
Statistics
Matches: 296, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 296 1.00
ACGTcount: A:0.50, C:0.02, G:0.16, T:0.32
Consensus pattern (6 bp):
TATAGA
Found at i:17833586 original size:19 final size:19
Alignment explanation
Indices: 17833562--17833601 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
17833552 CTTAATTTTG
17833562 ATCAAATAAAATT-AAATTA
1 ATCAAAT-AAATTAAAATTA
*
17833581 ATCAAATCAATTAAAATTA
1 ATCAAATAAATTAAAATTA
17833600 AT
1 AT
17833602 ATGATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (19 bp):
ATCAAATAAATTAAAATTA
Found at i:17834093 original size:17 final size:17
Alignment explanation
Indices: 17834048--17834148 Score: 53
Period size: 17 Copynumber: 5.6 Consensus size: 17
17834038 GCATTTTATT
*
17834048 AATTTAATATTAAAGTGA
1 AATTTAATATTAAA-TTA
*
17834066 TTATCTTAATATTAAATTA
1 -AAT-TTAATATTAAATTA
*
17834085 AATTTAATATT-TATCTA
1 AATTTAATATTAAAT-TA
* * *
17834102 CATTCTATTATTTTAA-TA
1 AATT-TAATA-TTAAATTA
*
17834120 AGATTTAATATTAAATTT
1 A-ATTTAATATTAAATTA
*
17834138 AATCTAATATT
1 AATTTAATATT
17834149 TATCTTGATA
Statistics
Matches: 63, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
16 2 0.03
17 26 0.41
18 14 0.22
19 9 0.14
20 12 0.19
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.50
Consensus pattern (17 bp):
AATTTAATATTAAATTA
Found at i:17834913 original size:49 final size:48
Alignment explanation
Indices: 17834787--17835037 Score: 211
Period size: 49 Copynumber: 5.2 Consensus size: 48
17834777 CCCCCGTGCA
* * * **
17834787 TCTGGGAGCAAGGTTAGTTTATTACTTTTCATAAGCCTCCCCTCATGTG
1 TCTGGGAGCAAGGTCACTTTATTACTTTCCATAAGCCTCCCC-CATACG
* *
17834836 T-TCGGGAGCAAGGCCACTTTACTACTTTCCATAAGCCTCCCCCATACG
1 TCT-GGGAGCAAGGTCACTTTATTACTTTCCATAAGCCTCCCCCATACG
* * * * * *
17834884 TCTGAGAGCAAGGTCACTTTCTTAGCTTT-CGTAAGCCTTCCCCTTACA
1 TCTGGGAGCAAGGTCACTTTATTA-CTTTCCATAAGCCTCCCCCATACG
* * * *
17834932 TCTGGGAGCAGGGTCACTTTATTACTTTCCGTAAGCCTCCTTCCATGCG
1 TCTGGGAGCAAGGTCACTTTATTACTTTCCATAAGCCTCC-CCCATACG
* * * * * * *
17834981 TCTAGGAACAAGTTTATTTTATTACTCTT-CATAAGTCTCCCCCCATGCG
1 TCTGGGAGCAAGGTCACTTTATTACT-TTCCATAAGCCT-CCCCCATACG
17835030 TCTGGGAG
1 TCTGGGAG
17835038 TAGGACATTC
Statistics
Matches: 161, Mismatches: 34, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
47 4 0.02
48 69 0.43
49 84 0.52
50 4 0.02
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.33
Consensus pattern (48 bp):
TCTGGGAGCAAGGTCACTTTATTACTTTCCATAAGCCTCCCCCATACG
Found at i:17834919 original size:48 final size:48
Alignment explanation
Indices: 17834769--17834971 Score: 160
Period size: 48 Copynumber: 4.2 Consensus size: 48
17834759 CTATCTTTTT
* * * * * * * *
17834769 GTAAGTCTCCCCCGTGCATCTGGGAGCAAGGTTAGTTTATTACTTTTC
1 GTAAGCCTCCCCCATACATCTGAGAGCAAGGTCACTTTCTTACTTTCC
* *** * *
17834817 ATAAGCCTCCCCTCATGTGT-TCGGGAGCAAGGCCACTTTAC-TACTTTCC
1 GTAAGCCTCCCC-CATACATCT-GAGAGCAAGGTCACTTT-CTTACTTTCC
* *
17834866 ATAAGCCTCCCCCATACGTCTGAGAGCAAGGTCACTTTCTTAGCTTT-C
1 GTAAGCCTCCCCCATACATCTGAGAGCAAGGTCACTTTCTTA-CTTTCC
* * * * *
17834914 GTAAGCCTTCCCCTTACATCTGGGAGCAGGGTCACTTTATTACTTTCC
1 GTAAGCCTCCCCCATACATCTGAGAGCAAGGTCACTTTCTTACTTTCC
17834962 GTAAGCCTCC
1 GTAAGCCTCC
17834972 TTCCATGCGT
Statistics
Matches: 126, Mismatches: 22, Indels: 14
0.78 0.14 0.09
Matches are distributed among these distances:
47 5 0.04
48 79 0.63
49 42 0.33
ACGTcount: A:0.20, C:0.30, G:0.19, T:0.31
Consensus pattern (48 bp):
GTAAGCCTCCCCCATACATCTGAGAGCAAGGTCACTTTCTTACTTTCC
Found at i:17835022 original size:96 final size:96
Alignment explanation
Indices: 17834839--17835015 Score: 205
Period size: 96 Copynumber: 1.8 Consensus size: 96
17834829 TCATGTGTTC
*
17834839 GGGAGCAAGGCCACTTTACTACTTTCCATAAGCCTCCCCCATACGTCTGAGAGCAAGGTCACTTT
1 GGGAGCAAGGCCACTTTACTACTTTCCATAAGCCTCCCCCATACGTCTGAGAACAAGGTCACTTT
* *
17834904 CTTAGCTTTCGTAAGCCTTCCCCTTACATCT
66 ATTAGCTTTCATAAGCCTTCCCCTTACATCT
* * * * * * * * *
17834935 GGGAGCAGGGTCACTTTATTACTTTCCGTAAGCCTCCTTCCATGCGTCT-AGGAACAAGTTTATT
1 GGGAGCAAGGCCACTTTACTACTTTCCATAAGCCTCC-CCCATACGTCTGA-GAACAAGGTCACT
17834999 TTATTA-CTCTTCATAAG
64 TTATTAGCT-TTCATAAG
17835016 TCTCCCCCCA
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
96 36 0.55
97 30 0.45
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.32
Consensus pattern (96 bp):
GGGAGCAAGGCCACTTTACTACTTTCCATAAGCCTCCCCCATACGTCTGAGAACAAGGTCACTTT
ATTAGCTTTCATAAGCCTTCCCCTTACATCT
Found at i:17838060 original size:12 final size:12
Alignment explanation
Indices: 17838035--17838073 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
17838025 ACTCGCTTCT
* *
17838035 TTACTTACTCAC
1 TTACTTGCTTAC
*
17838047 TTACTTGTTTAC
1 TTACTTGCTTAC
17838059 TTACTTGCTTAC
1 TTACTTGCTTAC
17838071 TTA
1 TTA
17838074 AATAAATCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:17838393 original size:50 final size:50
Alignment explanation
Indices: 17838283--17838464 Score: 188
Period size: 50 Copynumber: 3.5 Consensus size: 50
17838273 TGCCAAAGCT
* * * * *
17838283 ATGTCCCAGACATAGTCTTACATGGGATGTTTTC-TGTA-CTGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATATAGATGCCAATGTC
* * *
17838332 ATATCCCAGACATGGTCTTACATGGGAGTTCTCATATAGGTGCCAACGTC
1 ATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATAGATGCCAATGTC
* **
17838382 ATGTCCCAGACATGGCCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGTC
1 ATGTCCCAGACATGGTCTTACATGGGAGTTCTCAT-A--T--A-GATGCCAATGTC
17838438 ATGTCCCAGACATGGTCTTACATGGGA
1 ATGTCCCAGACATGGTCTTACATGGGA
17838465 TCTCATTCCC
Statistics
Matches: 111, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
48 5 0.05
49 28 0.25
50 39 0.35
51 1 0.01
53 1 0.01
55 1 0.01
56 36 0.32
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (50 bp):
ATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATAGATGCCAATGTC
Found at i:17845085 original size:46 final size:46
Alignment explanation
Indices: 17845067--17845361 Score: 374
Period size: 46 Copynumber: 6.3 Consensus size: 46
17845057 TGACAAGTGG
* * * *
17845067 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCAGCTACATTTATCTGATCAAGTGAC
* *
17845113 AAAGTGATAAGTGATAGCTTCGGCTATATTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCAGCTACATTTATCTGATCAAGTGAC
* * *
17845159 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCAGCTACATTTATCTGATCAAGTGAC
*
17845205 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCAGCTACATTTATCTGATCAAGTGAC
* * * *
17845251 AAGTGGAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 ------AAAGTGATAAGTGATAGCTTCAGCTACATTTATCTGATCAAGTGAC
* * * *
17845303 AAAGTGATAAGTGATAGCTTTAGTTACACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGCTTCAGCTACATTTATCTGATCAAGTGAC
17845349 AAAGTGATAAGTG
1 AAAGTGATAAGTG
17845362 GCTACACTTA
Statistics
Matches: 231, Mismatches: 12, Indels: 12
0.91 0.05 0.05
Matches are distributed among these distances:
46 188 0.81
52 43 0.19
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTTCAGCTACATTTATCTGATCAAGTGAC
Found at i:17845121 original size:98 final size:98
Alignment explanation
Indices: 17845001--17845350 Score: 559
Period size: 98 Copynumber: 3.6 Consensus size: 98
17844991 TTTGAGTACT
* * *
17845001 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACATTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
*
17845066 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 GAAAGTGATAAGTGATAGCTTCGGCTATACTTA
* * *
17845099 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTATATTTATCTGATCAAGTGAC-----
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
17845159 -AAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 GAAAGTGATAAGTGATAGCTTCGGCTATACTTA
17845191 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
17845256 GAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 GAAAGTGATAAGTGATAGCTTCGGCTATACTTA
* * * *
17845289 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGTTACACTTATCTGATCAAGAGACAA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAA
17845351 AGTGATAAGT
Statistics
Matches: 234, Mismatches: 12, Indels: 12
0.91 0.05 0.05
Matches are distributed among these distances:
92 88 0.38
98 146 0.62
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
GAAAGTGATAAGTGATAGCTTCGGCTATACTTA
Found at i:17845192 original size:92 final size:92
Alignment explanation
Indices: 17845067--17845361 Score: 464
Period size: 92 Copynumber: 3.1 Consensus size: 92
17845057 TGACAAGTGG
*
17845067 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCT
1 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCT
* * *
17845132 TCGGCTATATTTATCTGATCAAGTGAC
66 TCAGCTACACTTATCTGATCAAGTGAC
17845159 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCT
1 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCT
17845224 TCAGCTACACTTATCTGATCAAGTGAC
66 TCAGCTACACTTATCTGATCAAGTGAC
*
17845251 AAGTGGAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 ------AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTG
* * *
17845316 ATAGCTTTAGTTACACTTATCTGATCAAGAGAC
60 ATAGCTTCAGCTACACTTATCTGATCAAGTGAC
17845349 AAAGTGATAAGTG
1 AAAGTGATAAGTG
17845362 GCTACACTTA
Statistics
Matches: 189, Mismatches: 8, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
92 101 0.53
98 88 0.47
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (92 bp):
AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCT
TCAGCTACACTTATCTGATCAAGTGAC
Found at i:17845261 original size:144 final size:138
Alignment explanation
Indices: 17845001--17845361 Score: 506
Period size: 144 Copynumber: 2.5 Consensus size: 138
17844991 TTTGAGTACT
* *
17845001 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACATTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-----
* * *
17845066 GAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGC
61 -AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGC
*
17845131 TTCGGCTATATTTA
125 TTCGGCTATACTTA
** *
17845145 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
17845210 GATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGC
66 GATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC------AAAGTGATAAGTGATAGC
17845275 TTCGGCTATACTTA
125 TTCGGCTATACTTA
* * *
17845289 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGTTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
17845354 GATAAGTG
66 GATAAGTG
17845362 GCTACACTTA
Statistics
Matches: 196, Mismatches: 15, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
138 43 0.22
144 153 0.78
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (138 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
GATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGC
TATACTTA
Found at i:17845338 original size:190 final size:190
Alignment explanation
Indices: 17845001--17845361 Score: 623
Period size: 190 Copynumber: 1.9 Consensus size: 190
17844991 TTTGAGTACT
* * *
17845001 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACATTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
*
17845066 GAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGC
66 GAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGC
* * * *
17845131 TTCGGCTATATTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTATACTTA
131 TTCAGCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCGGCTATACTTA
17845191 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
*
17845256 GAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGC
66 GAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGC
* *
17845321 TTTAGTTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
131 TTCAGCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
17845362 GCTACACTTA
Statistics
Matches: 160, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
190 160 1.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (190 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
GAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGC
TTCAGCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCGGCTATACTTA
Found at i:17845377 original size:37 final size:37
Alignment explanation
Indices: 17845327--17845433 Score: 173
Period size: 37 Copynumber: 2.9 Consensus size: 37
17845317 TAGCTTTAGT
17845327 TACACTTATCTGATCAAGAGACAAAGTGATAAGTGGC
1 TACACTTATCTGATCAAGAGACAAAGTGATAAGTGGC
*
17845364 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGC
1 TACACTTATCTGATCAAGAGACAAAGTGATAAGTGGC
* *
17845401 TACACTTATCTGATC-AGGGA-TAAGTGATAAGTG
1 TACACTTATCTGATCAAGAGACAAAGTGATAAGTG
17845434 ATCATACGTA
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
35 12 0.18
36 3 0.05
37 51 0.77
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.26
Consensus pattern (37 bp):
TACACTTATCTGATCAAGAGACAAAGTGATAAGTGGC
Found at i:17846777 original size:21 final size:21
Alignment explanation
Indices: 17846737--17846778 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
17846727 CCATATTTAT
*
17846737 TTTAATTTATTTGATTTTGAA
1 TTTAATTTATTTGATGTTGAA
17846758 TTTAATTTAATTT-ATGTTGAA
1 TTTAATTT-ATTTGATGTTGAA
17846779 AATAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.60
Consensus pattern (21 bp):
TTTAATTTATTTGATGTTGAA
Found at i:17850441 original size:28 final size:28
Alignment explanation
Indices: 17850389--17850457 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
17850379 AAATAAAAAA
*
17850389 TTACCAAAATGT-TATAACTTTTTTTAT
1 TTACCAAAATATATATAACTTTTTTTAT
*
17850416 TTACCAAAATATATATAATTTTTTTTAT
1 TTACCAAAATATATATAACTTTTTTTAT
17850444 TTACCAAAATATAT
1 TTACCAAAATATAT
17850458 CAAAAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 11 0.28
28 28 0.72
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.49
Consensus pattern (28 bp):
TTACCAAAATATATATAACTTTTTTTAT
Found at i:17850476 original size:13 final size:12
Alignment explanation
Indices: 17850459--17850493 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
17850449 AAAATATATC
17850459 AAAAAAAAACAA
1 AAAAAAAAACAA
*
17850471 ACAAAAAAAACAG
1 A-AAAAAAAACAA
17850484 AAAAAAAAAC
1 AAAAAAAAAC
17850494 CTGAACTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.86, C:0.11, G:0.03, T:0.00
Consensus pattern (12 bp):
AAAAAAAAACAA
Found at i:17850560 original size:27 final size:28
Alignment explanation
Indices: 17850522--17850599 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 28
17850512 TCTCTGGGTG
17850522 GAGGGAAGCAGGTTGGCGGCACCAAACA
1 GAGGGAAGCAGGTTGGCGGCACCAAACA
* ***
17850550 G-GGGAAGCAGGTTGGCAGCACC-AGTG
1 GAGGGAAGCAGGTTGGCGGCACCAAACA
*
17850576 GAGGGAACCAGGTTGGCGGCACCA
1 GAGGGAAGCAGGTTGGCGGCACCA
17850600 CCCTTGAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
26 2 0.05
27 39 0.93
28 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.42, T:0.09
Consensus pattern (28 bp):
GAGGGAAGCAGGTTGGCGGCACCAAACA
Found at i:17850688 original size:14 final size:14
Alignment explanation
Indices: 17850654--17850745 Score: 71
Period size: 14 Copynumber: 6.4 Consensus size: 14
17850644 GGGGAAGAAG
*
17850654 AAGAAAGAAAAAGAAA
1 AAGAAAG-AAAAG-GA
*
17850670 AAGAAGGAAAAGGA
1 AAGAAAGAAAAGGA
*
17850684 AAGAAAGAAAAAGA
1 AAGAAAGAAAAGGA
*
17850698 AGGAAAGAAAAGGA
1 AAGAAAGAAAAGGA
** *
17850712 AAGGGGAGGAAA-GA
1 AA-GAAAGAAAAGGA
17850726 AAGAAA-AATAAGGA
1 AAGAAAGAA-AAGGA
17850740 AAGAAA
1 AAGAAA
17850746 AGGAAAGGAG
Statistics
Matches: 60, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
12 1 0.02
13 4 0.07
14 38 0.63
15 11 0.18
16 6 0.10
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (14 bp):
AAGAAAGAAAAGGA
Found at i:17850692 original size:18 final size:18
Alignment explanation
Indices: 17850679--17850745 Score: 80
Period size: 18 Copynumber: 3.6 Consensus size: 18
17850669 AAAGAAGGAA
17850679 AAGGAAAGAAAGAAAAAG
1 AAGGAAAGAAAGAAAAAG
**
17850697 AAGGAAAGAAAAGGAAAGGG
1 AAGGAAAG-AAA-GAAAAAG
* *
17850717 GAGGAAAGAAAGAAAAAT
1 AAGGAAAGAAAGAAAAAG
17850735 AAGGAAAGAAA
1 AAGGAAAGAAA
17850746 AGGAAAGGAG
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
18 22 0.55
19 6 0.15
20 12 0.30
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.01
Consensus pattern (18 bp):
AAGGAAAGAAAGAAAAAG
Found at i:17850710 original size:10 final size:10
Alignment explanation
Indices: 17850663--17850752 Score: 75
Period size: 10 Copynumber: 9.4 Consensus size: 10
17850653 GAAGAAAGAA
*
17850663 AAAGAAAAAG
1 AAAGAAAAGG
*
17850673 AAGGAAAAGG
1 AAAGAAAAGG
17850683 AAAG-AAA-G
1 AAAGAAAAGG
17850691 AAA-AAGAAGG
1 AAAGAA-AAGG
17850701 AAAGAAAAGG
1 AAAGAAAAGG
***
17850711 AAAGGGGAGG
1 AAAGAAAAGG
17850721 AAAG-AAA-G
1 AAAGAAAAGG
17850729 AAA-AATAAGG
1 AAAGAA-AAGG
17850739 AAAGAAAAGG
1 AAAGAAAAGG
17850749 AAAG
1 AAAG
17850753 GAGAAGCGAA
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
8 10 0.16
9 8 0.12
10 42 0.66
11 4 0.06
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (10 bp):
AAAGAAAAGG
Found at i:17850713 original size:24 final size:24
Alignment explanation
Indices: 17850654--17850714 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
17850644 GGGGAAGAAG
*
17850654 AAGAAAGAAAAAGAAAAAGAAGGAA
1 AAGAAA-AGAAAGAAAAAGAAGGAA
*
17850679 AAGGAAAGAAAGAAAAAGAAGG-A
1 AAGAAAAGAAAGAAAAAGAAGGAA
17850702 AAGAAAAGGAAAG
1 AAGAAAA-GAAAG
17850715 GGGAGGAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.22
24 20 0.62
25 5 0.16
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (24 bp):
AAGAAAAGAAAGAAAAAGAAGGAA
Found at i:17850722 original size:38 final size:38
Alignment explanation
Indices: 17850679--17850807 Score: 151
Period size: 38 Copynumber: 3.4 Consensus size: 38
17850669 AAAGAAGGAA
17850679 AAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGG
1 AAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGG
* *
17850717 GAGGAAAGAAAGAAAAATAAGGAAAGAAAAGGAAAGGAG
1 AAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGG-G
*
17850756 AAGCG-AA-AAA-AAAAAGAAGAAGAAGAAGAAGG-AA-GG
1 AAG-GAAAGAAAGAAAAAGAAGGA-AAGAA-AAGGAAAGGG
*
17850792 AAGGAAAAAAAGAAAA
1 AAGGAAAGAAAGAAAA
17850808 TAAGGTAATT
Statistics
Matches: 79, Mismatches: 5, Indels: 14
0.81 0.05 0.14
Matches are distributed among these distances:
35 1 0.01
36 6 0.08
37 13 0.16
38 49 0.62
39 9 0.11
40 1 0.01
ACGTcount: A:0.67, C:0.01, G:0.31, T:0.01
Consensus pattern (38 bp):
AAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGG
Found at i:17850749 original size:28 final size:27
Alignment explanation
Indices: 17850669--17850752 Score: 80
Period size: 28 Copynumber: 3.0 Consensus size: 27
17850659 AGAAAAAGAA
* *
17850669 AAAGAAGGAAAAGGAAAGAAAGAAAAAG
1 AAAGAAAGAAAAGGAAAGAAAG-GAAAG
* **
17850697 AAGGAAAGAAAAGGAAAGGGGAGGAAAG
1 AAAGAAAGAAAAGGAAA-GAAAGGAAAG
17850725 AAAGAAA-AATAAGGAAAGAAAAGGAAAG
1 AAAGAAAGAA-AAGGAAAG-AAAGGAAAG
17850753 GAGAAGCGAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
27 3 0.07
28 39 0.87
29 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (27 bp):
AAAGAAAGAAAAGGAAAGAAAGGAAAG
Found at i:17851521 original size:19 final size:19
Alignment explanation
Indices: 17851473--17851524 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
17851463 AAAATATATA
** *
17851473 TAATATTTTGGTATTTTTT
1 TAATATTTTATTATTTTTG
17851492 TAATATTTTATTATTTTTG
1 TAATATTTTATTATTTTTG
*
17851511 TAATGTTTTATTAT
1 TAATATTTTATTAT
17851525 GGGTTTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (19 bp):
TAATATTTTATTATTTTTG
Found at i:17851610 original size:27 final size:28
Alignment explanation
Indices: 17851560--17851628 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
17851550 AAATAAAAAA
17851560 TTACCAAAATAT-TATAACTTTTTTTTAT
1 TTACCAAAATATATATAAC-TTTTTTTAT
17851588 TTACCAAAATATATATAA-TTTTTTTAT
1 TTACCAAAATATATATAACTTTTTTTAT
*
17851615 TTATCAAAATATAT
1 TTACCAAAATATAT
17851629 CAAAAAAAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 22 0.56
28 12 0.31
29 5 0.13
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.51
Consensus pattern (28 bp):
TTACCAAAATATATATAACTTTTTTTAT
Found at i:17852257 original size:15 final size:14
Alignment explanation
Indices: 17852217--17852245 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
17852207 TTTTTGTATC
17852217 AATTTAATTATTCT
1 AATTTAATTATTCT
17852231 AATTTAATTATTCT
1 AATTTAATTATTCT
17852245 A
1 A
17852246 GTTTTAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTAATTATTCT
Found at i:17852688 original size:27 final size:27
Alignment explanation
Indices: 17852658--17852736 Score: 113
Period size: 27 Copynumber: 2.9 Consensus size: 27
17852648 GGCAGGACTA
*
17852658 GTGCCGCCAACCTGGTTCCCTCCACTG
1 GTGCCGCCAACCTGCTTCCCTCCACTG
****
17852685 GTGCCGCCAACCTGCTTCCCTTGTTTG
1 GTGCCGCCAACCTGCTTCCCTCCACTG
17852712 GTGCCGCCAACCTGCTTCCCTCCAC
1 GTGCCGCCAACCTGCTTCCCTCCAC
17852737 CTAGGGAGTT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.10, C:0.44, G:0.20, T:0.25
Consensus pattern (27 bp):
GTGCCGCCAACCTGCTTCCCTCCACTG
Found at i:17861510 original size:20 final size:19
Alignment explanation
Indices: 17861475--17861523 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
17861465 TTTTTTTTAG
*
17861475 ATTTTTTTA-CTTTTTAAC
1 ATTTTTTTATATTTTTAAC
**
17861493 ATTTTTTTATATTCTTTAGG
1 ATTTTTTTATATT-TTTAAC
17861513 ATTTTTTTATA
1 ATTTTTTTATA
17861524 ATTTCTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 9 0.35
19 2 0.08
20 15 0.58
ACGTcount: A:0.22, C:0.06, G:0.04, T:0.67
Consensus pattern (19 bp):
ATTTTTTTATATTTTTAAC
Found at i:17861567 original size:17 final size:17
Alignment explanation
Indices: 17861545--17861587 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
17861535 TGTTAAAAAA
*
17861545 TATAAATTTTGGATTTT
1 TATAAATTTTGGAATTT
*
17861562 TATAAATATTTTGAATTT
1 TATAAAT-TTTGGAATTT
*
17861580 TAAAAATT
1 TATAAATT
17861588 ATTTTGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (17 bp):
TATAAATTTTGGAATTT
Found at i:17861572 original size:19 final size:20
Alignment explanation
Indices: 17861550--17861605 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
17861540 AAAAATATAA
* *
17861550 ATTTTGGATTTTTATAAA-T
1 ATTTTGGAATTTTAAAAATT
17861569 ATTTT-GAATTTTAAAAATT
1 ATTTTGGAATTTTAAAAATT
*
17861588 ATTTTGAAAATTTTAAAA
1 ATTTTG-GAATTTTAAAA
17861606 TTACCTGTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 10 0.32
19 11 0.35
21 10 0.32
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (20 bp):
ATTTTGGAATTTTAAAAATT
Found at i:17861601 original size:21 final size:18
Alignment explanation
Indices: 17861559--17861605 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 18
17861549 AATTTTGGAT
*
17861559 TTTTATAAATATTTTGAA
1 TTTTAAAAATATTTTGAA
17861577 TTTTAAAAATTATTTTGAAAA
1 TTTTAAAAA-TATTTTG--AA
17861598 TTTTAAAA
1 TTTTAAAA
17861606 TTACCTGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 8 0.32
19 7 0.28
21 10 0.40
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (18 bp):
TTTTAAAAATATTTTGAA
Found at i:17867261 original size:27 final size:27
Alignment explanation
Indices: 17867205--17867258 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 27
17867195 ATTTTAAAAG
*
17867205 ATTCTTTTAACTATAACTTAGGGATCA
1 ATTCTTTTAACTATAACTTAAGGATCA
17867232 ATTCTTTTAACTA-AACTTAAGGATCA
1 ATTCTTTTAACTATAACTTAAGGATCA
17867258 A
1 A
17867259 ATTAGCTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (27 bp):
ATTCTTTTAACTATAACTTAAGGATCA
Found at i:17867661 original size:20 final size:21
Alignment explanation
Indices: 17867633--17867677 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
17867623 ATGAAACCAA
17867633 TTTATTTTTTC-TAATTTTCAT
1 TTTATTTTTTCATAATTTT-AT
*
17867654 TTTA-TTTTTCATTATTTTAT
1 TTTATTTTTTCATAATTTTAT
17867674 TTTA
1 TTTA
17867678 AAGTTCTCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTATTTTTTCATAATTTTAT
Found at i:17870348 original size:77 final size:78
Alignment explanation
Indices: 17870200--17870356 Score: 298
Period size: 77 Copynumber: 2.0 Consensus size: 78
17870190 TCAGTCTTAG
17870200 TTATTAGCAAATTTTGAAAACAAAGTACTGACATCTCAAATGATAGGAAATCTTAGAAATAACAA
1 TTATTAGCAAATTTTGAAAACAAAGTACTGACATCTCAAATGATAGGAAATCTTAGAAATAACAA
17870265 TTCTGTTAATACT
66 TTCTGTTAATACT
*
17870278 TTATTAGCAAATTTTGAAAACAAAGTACTGACATTTC-AATGATAGGAAATCTTAGAAATAACAA
1 TTATTAGCAAATTTTGAAAACAAAGTACTGACATCTCAAATGATAGGAAATCTTAGAAATAACAA
17870342 TTCTGTTAATACT
66 TTCTGTTAATACT
17870355 TT
1 TT
17870357 CTTCCAATAC
Statistics
Matches: 78, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
77 42 0.54
78 36 0.46
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (78 bp):
TTATTAGCAAATTTTGAAAACAAAGTACTGACATCTCAAATGATAGGAAATCTTAGAAATAACAA
TTCTGTTAATACT
Found at i:17879980 original size:245 final size:245
Alignment explanation
Indices: 17879541--17879996 Score: 887
Period size: 245 Copynumber: 1.9 Consensus size: 245
17879531 ATCGTGCTAA
17879541 AAAGACCATTAAATAAATTTCTTACCCTTTAGCAATTTATTCTACAAAGACTAAACTCATTAAAT
1 AAAGACCATTAAATAAATTTCTTACCCTTTAGCAATTTATTCTACAAAGACTAAACTCATTAAAT
17879606 TCAAGAAAAACACATGCAAATATGGTTGAGTCATTTCCTAAGATGATAGTTTGCATGTTTTATTT
66 TCAAGAAAAACACATGCAAATATGGTTGAGTCATTTCCTAAGATGATAGTTTGCATGTTTTATTT
17879671 TAATTTTTTCTTTTCAATTTTTGCATGATGTATGTAATTTGCATGAAATCTACACTTGTTGAGAT
131 TAATTTTTTCTTTTCAATTTTTGCATGATGTATGTAATTTGCATGAAATCTACACTTGTTGAGAT
17879736 GTTGAATTATTTGTCTGATGGAGGAATGCGGTAAATAAGCTTGTGAGAAT
196 GTTGAATTATTTGTCTGATGGAGGAATGCGGTAAATAAGCTTGTGAGAAT
*
17879786 AAAGCACCA-TAAATAAATTTCTTACCCTTTAGCAATTTATTCTACAAAGACTAAACTTATTAAA
1 AAAG-ACCATTAAATAAATTTCTTACCCTTTAGCAATTTATTCTACAAAGACTAAACTCATTAAA
17879850 TTCAAGAAAAACACATGCAAATATGGTTGAGTCATTTCCTAAGATGATAGTTTGCATGTTTTATT
65 TTCAAGAAAAACACATGCAAATATGGTTGAGTCATTTCCTAAGATGATAGTTTGCATGTTTTATT
17879915 TTAATTTTTTCTTTTCAATTTTTGCATGATGTATGTAATTTGCATGAAATCTACACTTGTTGAGA
130 TTAATTTTTTCTTTTCAATTTTTGCATGATGTATGTAATTTGCATGAAATCTACACTTGTTGAGA
17879980 TGTTGAATTATTTGTCT
195 TGTTGAATTATTTGTCT
17879997 CTGTCTGAGA
Statistics
Matches: 209, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
245 205 0.98
246 4 0.02
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (245 bp):
AAAGACCATTAAATAAATTTCTTACCCTTTAGCAATTTATTCTACAAAGACTAAACTCATTAAAT
TCAAGAAAAACACATGCAAATATGGTTGAGTCATTTCCTAAGATGATAGTTTGCATGTTTTATTT
TAATTTTTTCTTTTCAATTTTTGCATGATGTATGTAATTTGCATGAAATCTACACTTGTTGAGAT
GTTGAATTATTTGTCTGATGGAGGAATGCGGTAAATAAGCTTGTGAGAAT
Found at i:17881543 original size:34 final size:34
Alignment explanation
Indices: 17881493--17881570 Score: 138
Period size: 34 Copynumber: 2.3 Consensus size: 34
17881483 CATTAATTTA
*
17881493 AAATACAACAATTAACAACTTGGTTCGGATTATAG
1 AAATACAA-AATTAACAACTAGGTTCGGATTATAG
17881528 AAATACAAAATTAACAACTAGGTTCGGATTATAG
1 AAATACAAAATTAACAACTAGGTTCGGATTATAG
17881562 AAATACAAA
1 AAATACAAA
17881571 CTAGAAATTC
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
34 34 0.81
35 8 0.19
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.26
Consensus pattern (34 bp):
AAATACAAAATTAACAACTAGGTTCGGATTATAG
Done.